To stash your working directory including untracked files (especially those that are in the .gitignore) then you probably want to use this cmd:
git stash --include-untracked
Update 17 May 2018:
New versions of git now have
git stash --all which stashes all files, including untracked and ignored files.
git stash --include-untracked no longer touches ignored files (tested on git 2.16.2).
Original answer below:
As of version 1.7.7 you can use
git stash --include-untracked or
git stash save -u to stash untracked files without staging them.
git add) the file and start tracking it. Then stash. Since the entire contents of the file are new, they will be stashed, and you can manipulate it as necessary.